Vivarium Dagger
This library builds and runs multi-step data pipelines. It provides dagger, a command that runs a pipeline described in a YAML file as one Jobmon workflow on a Slurm cluster.
Supported Python versions: 3.11, 3.12, 3.13
You can install vivarium-dagger from PyPI with pip:
pip install vivarium-daggeror build it from source by cloning the monorepo and installing this package:
git clone https://github.com/ihmeuw/vivarium-suite.git
cd vivarium-suite
pip install libs/daggerMulti-step workflows with dagger
A dagger workflow file lists steps that run in order. Each step gives its command and its compute resources:
workflow:
name: my_pipeline
project: proj_simscience
queue: all.q
output_directory: /path/to/output
steps:
- name: run_sims
type: simulation
resources:
memory_gb: 3
runtime: "24:00:00"
args:
model_specification: /path/to/model_specification.yaml
branch_configuration: /path/to/branches.yaml
- name: post_process
command: my_post_processing_script /path/to/output
resources:
memory_gb: 8
runtime: "00:30:00"Launch the workflow with
dagger run -c /path/to/workflow.yamlIf a run fails partway through, resume it from its output directory, skipping steps that already completed, with
dagger restart /path/to/outputCheck out the docs!
1 maintainer
Metadata
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Release files for vivarium-dagger 0.1.0
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| File | Size | Uploaded | Provenance | Actions |
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| vivarium_dagger-0.1.0-py3-none-any.whl | Python 3 | none | any | Details for vivarium_dagger-0.1.0-py3-none-any.whl |
Total release size: 100.9 kB
Release files / vivarium_dagger-0.1.0.tar.gz
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| Tags | Python 3 |
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